AbstractThe applicability of the temperature proxy based on a tetraether index of 86 carbon atoms (TEX86) from isoprenoidal glycerol dialkyl glycerol tetraethers (isoGDGTs) has increasingly been examined in the South China Sea (SCS). Views on the proxy differ on whether it is biased to a particular season or to depth in this sea. Here we studied isoGDGTs in a large number of suspended particulate matters (SPM) in surface water during summer and winter as well as several surface sediments of the northern SCS. The integration of these novel data with already published data demonstrated that isoGDGTs were similar in distribution between surface water SPM and shallow shelf sediments. They can be characterized by low ratio (<4) of [GDGT‐2]/[GDGT‐3] and low‐percentage abundance (<4%) of the crenarchaeol regioisomer; however, those in deep basin sediments showed higher values for both parameters, suggesting a substantial contribution of “deep‐water” Thaumarchaeota. The relationship between TEX86 in SPM and in situ measured sea surface temperature differed from a global calibration and showed distinct trends between summer and winter, reflecting archaeal seasonality in surface waters. By assuming the TEX86 temperature signal in shallow sediments as the weighted mean of summer and winter signals, we revealed spatial changes in the relative contribution of summer and winter archaeal isoGDGTs to sediments, with a likely higher winter contribution further offshore. This occurrence may complicate the interpretation of the shallow sedimentary TEX86 record, and further investigation is required to fully understand seasonal archaeal lipid production and sedimentation.